Ex Parte LO et al

Patent Trials and Appeals Board

Jun 6, 2019

14599082 - (D) (P.T.A.B. Jun. 6, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/599,082 01/16/2015 YUK MING DENNIS LO
20350 7590 06/10/2019
KILPATRICK TOWNSEND & STOCKTONLLP
Mailstop: IP Docketing - 22
1100 Peachtree Street
Suite 2800
Atlanta, GA 30309
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www .uspto.gov
ATTORNEY DOCKET NO. CONFIRMATION NO.
80015-929799-002514US 7748
EXAMINER
GOLDBERG, JEANINE ANNE
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
06/10/2019 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
ipefiling@kilpatricktownsend.com
KTSDocketing2@kilpatrick.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte YUK MING DENNIS LO and LIT MAN POON
Appeal 2018-003411
Application 14/599,082
Technology Center 1600
Before DEBORAH KATZ, ULRIKE W. JENKS, and JOHN G. NEW,
Administrative Patent Judges.
KATZ, Administrative Patent Judge.
DECISION ON APPEAL
Appeal 2018-003411
Application 14/599,082
Introduction
Appellants 1 seek our review, under 35 U.S.C. § 134(a), of the
Examiner's decision to reject claims 39-56 (Appeal Brief filed July 27, 2017
("App. Br.") 5.)
We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM.
The Examiner rejects the claims as follows (Final Office Action
mailed February 6, 2017 ("Final Act.") 3-23):
39-56
39--41,
48, 49,
54,55
39--44,
49, 50,
52,53
39-56
Lo Coco2
Turhan3
U.S. Pat. No. 8,962,280,
Claims 1-14
U.S. Pat. No. 6,927,028,
Claims 1, 3, 5-7, 24--26
U.S. Pat. No. 8,431,343,
Claims 1-9
U.S. Pat. No. 7,709,197,
Claims 1-5
U.S. Pat. No. 7,901,884,
Claims 1-27
35 U.S.C. § 101 3-12
35 U.S.C. § 102(b) 12-14
(pre-AIA)
35 U.S.C. § 102(b) 14--15
(pre-AIA)
Obviousness-type 15-24
Double Patenting
1 Appellants report that the real party in interest is The Chinese
University of Hong Kong. (App. Br. 3.)
2 Lo Coco et al., Polyclonal Hematopoietic Reconstitution in Leukemia
Patients at Remission After Suppression of Specific Gene Rearrangements,
82 Blood 606----612 (1993).
3 Turhan et al., Transient Suppression of Clonal Hemopoiesis Associated
with Pregnancy in a Patient with a Myeloproliferative Disorder, 81 Journal
of Clinical Investigation 1999-2003 (1988).
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Application 14/599,082
I
U.S. Pat. No. 8,026,067,
. Claims 1-22
Appellants' Specification provides methods for differentiating DNA
species originating from different individuals in a biological sample by
observing epigenetic differences in DNA methylation. (Specification
("Spec.") ,r 7.) The Specification explains that "[t]he presence of DNA
originating from different individuals in bodily fluids is a well-known
biological phenomenon in many clinical and biological scenarios." (Spec.
,r 2.) The phenomenon may occur following bone marrow transplantation
from a donor or during pregnancy. (See id. ,r,r 2-3.) Detection of fetal DNA
in maternal plasma and serum has been used for non-invasive prenatal
diagnosis. (Id. ,r 3.) However, "[a]ll of these current approaches have
utilized the detection of DNA sequences inherited from the father and which
are genetically distinguishable from those of the mother ... [and], the
detection of DNA that the fetus has inherited from the mother in maternal
plasma or serum has been thought to be impossible." (Id.) The
Specification argues that "discriminating DNA species originating from
different individuals in biological fluids using epigenetic, rather than genetic
differences ... would provide a significant advancement enabling additional
screening and diagnostic methods." (Id. ,r 5.)
Appellants' claim 39 recites:
A method for determining methylation status of a cell-
free human DNA species in a biological sample that (1)
contains cell-free human DNA originated from two different
human individuals and (2) is obtained from one of the two
different human individuals, the method comprising the steps
of:
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Application 14/599,082
(a) treating the cell-free human DNA from the sample
with a reagent that differentially reacts with methylated and
unmethylated DNA; and
(b) detecting the presence of a methylated version and/or
an unmethylated version of the cell-free human DNA species in
the sample, thereby determining methylation status of the
human DNA species in the sample.
(Amendment filed January 3, 2017.)4
Appellants do not present separate arguments against the rejections of
the dependent claims. We focus on claim 39 in our analysis below. See 37
C.F.R. § 4I.37(c)(l)(iv).
Analysis
35 U.S.C. § 101, Non-Statutory Subject Matter
The Examiner rejects claims 39-56 under 35 U.S.C. § 101 as being
directed to non-statutory subject matter. (Final Act. 3.) Although 35 U.S.C.
§ 101 provides that "[ w ]hoever invents or discovers any new and useful
process, machine, manufacture, or composition of matter, or any new and
useful improvement thereof, may obtain a patent therefor ... ," the Supreme
Court has determined that there are exceptions to what is patentable.
Specifically, "laws of nature, natural phenomena, and abstract ideas" are not
eligible subject matter. See Diamond v. Diehr, 450 U.S. 175, 185 (1981).
To determine if claimed subject matter is statutorily eligible in light of these
judicial exceptions the Supreme Court has articulated a two-step framework
4 Appellants acknowledge that claim 39 listed in the Appeal Brief incorrectly
included subject matter submitted in an After-Final Amendment that was not
entered (See Reply Brief filed February 8, 2018 ("Reply Br.") 5; see also
Examiner's Answer mailed December 19, 2017 ("Ans.") 3.)
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Application 14/599,082
in Mayo Collaborative Services v. Prometheus Labs., Inc., 566 U.S. 66
(2012), and later cases. Specifically,
[f]irst, we determine whether the claims at issue are directed to
one of those patent-ineligible concepts .... If so, we then ask,
"[w]hat else is there in the claims before us?" ... To answer
that question, we consider the elements of each claim both
individually and "as an ordered combination" to determine
whether the additional elements "transform the nature of the
claim" into a patent-eligible application.
Alice Corp. Pty. v. CLS Banklnt'l, 573 U.S. 208, 2355 (2014) (quoting
Mayo, 566 U.S. at 78). Thus, we must determine whether the claim is
directed to a judicially determined patent-ineligible concept and, if so, then
ask if there is anything in the claim that transforms it into patent-eligible
subject matter.
The USPTO recently published revised guidance on the application of
§ 101. See 2019 Revised Patent Subject Matter Eligibility Guidance, 84
Fed. Reg. 50-57 (2019) ("2019 Guidelines"). After determining that
claimed subject matter falls within one of the four categories of patentable
subject matter identified in 35 U.S.C. § 101, the 2019 Guidelines provides a
"revised step 2A." which corresponds to the first step of the Alice/Mayo test
articulated above, to determine whether a claim is directed to a judicial
exception. (See 2019 Guidelines, 84 Fed. Reg. 50, 53-54.) In a first prong
of revised step 2A, the examiner must determine whether the claim recites a
judicial exception. (See id. at 54.) If a judicial exception is identified, the
second prong requires a determination of whether the judicial exception is
integrated into a practical application. (See id.) If so, the inquiry ends and
the claim is determined to be directed to eligible subject matter under the
2019 Guidelines. (See id. at 54 ("When the exception is so integrated [into a
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practical application], then the claim is not directed to a judicial exception
(Step 2A: NO) and is eligible. This concludes the eligibility analysis.").) If
not, the analysis continues to determine if the claim provides an inventive
concept. (See id. at 56.)
The Examiner finds Appellants' claims are directed to the natural
phenomenon of methylated cell-free DNA (cf-DNA) which circulates in the
blood stream of pregnant women and transplant patients. (Final Act. 5.)
The Examiner finds the claims do not "provide a method which is
significantly more from a statement of a natural principle." (See Final Act.
6.) In particular, the Examiner finds the "method at issue here amounts to a
general instruction to practitioners to apply routine, conventional techniques
when seeking to detect [cf-DNA] methylation." (See Final Act. 10.) To
support the finding that methylation analysis was well-understood, routine
and conventional activity in 2001, the Examiner cites Turhan and Lo Coco,
addressed in the anticipation discussion below, among other references cited
during the prosecution of the application. (See Final Act. 6-10.)
In making the rejection, the Examiner relies on Ariosa Diagnostics,
Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). (See Final Act. 10.)
In Ariosa, our reviewing court found Sequenom' s claims did not recite
patent eligible subject matter, because "[t]he existence and location of
cfIDNA is a natural phenomenon [and] identifying its presence was merely
claiming the natural phenomena itself." Rapid Litig. Mgmt. Ltd. v.
CellzDirect, Inc., 827 F.3d 1042, 1048 (Fed. Cir. 2016) (citing Ariosa, 788
F.3d at 1376). Claim 1, a representative claim, at issue inAriosa recited:
A method for detecting a paternally inherited nucleic acid of
fetal origin performed on a maternal serum or plasma sample
from a pregnant female, which method comprises amplifying a
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Application 14/599,082
paternally inherited nucleic acid from the serum or plasma
sample and detecting the presence of a paternally inherited
nucleic acid of fetal origin in the sample.
Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1373-74 (Fed.
Cir. 2015). Like the claims at issue in Ariosa, Appellants' currently pending
claims recite a method of detecting nucleic acid originating from a natural
source other than the subject providing the sample and characterizing it.
Appellants argue that the Examiner erred in following the Federal
Circuit's reasoning inAriosa because "Ariosa is inconsistent with Mayo and
therefore must be disregarded in favor of Mayo." (App. Br. 7.) We are not
persuaded that the reasoning in Ariosa was inconsistent with the reasoning in
Mayo. The Ariosa court expressly followed Mayo, stating that "the Supreme
Court set forth a framework for distinguishing patents that claim laws of
nature, natural phenomena, and abstract ideas from those that claim patent-
eligible applications of those concepts." (Ariosa, 788 F.3d at 1375.) The
Ariosa court explained that under the first step of the Mayo framework, the
claimed method falls within an exception to the broad definition of eligible
subject matter in 35 U.S.C. § 101 because it is directed to matter that is
naturally occurring. See id. at 1376 ("The method ends with paternally
inherited cfIDNA, which is also a natural phenomenon. The method
therefore begins and ends with a natural phenomenon. Thus, the claims are
directed to matter that is naturally occurring."). The court continued by
determining that under the second step of the Mayo framework, "the practice
of the method steps does not result in an inventive concept that transforms
the natural phenomenon of cfIDNA into a patentable invention." (Id.)
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Thus, the Ariosa court followed the two-step framework prescribed in
Mayo and we disagree that the decision in Ariosa must be disregarded. (See
id. at 1381 (Linn, J., concurring) ("The Supreme Court's blanket dismissal
of conventional post-solution steps leaves no room to distinguish Mayo from
this case, even though here no one was amplifying and detecting paternally-
inherited cfIDNA using the plasma or serum of pregnant mothers.").)
Appellants also argue that their claimed method does not recite a
judicial exception to 35 U.S.C. § 101 in light of Example 29 of the May
2016 Subject Matter Eligibility Examples: Life Sciences ("May 2016
Examples"). (App. Br. 6.) According to Appellants, the absence of a step
correlating an observed change with a disease indicates it is patentable. (Id.,
citing Mayo, 566 U.S. at 78.) Even if the presence or absence of a
correlating step were the sole determiner of eligibility, Appellants' claims
include the correlation step of determining methylation status based on the
detection of a methylated and/or an unmethylated version of cell-free human
DNA in a sample. Thus, claim 1 of Example 29, which includes only the
steps of obtaining a sample and detecting whether JUL-I is present, is not
informative for Appellants' pending claims. Example 29 does not indicate
that Appellants' claims are directed to eligible subject matter.
We tum to the analysis of eligibility of Appellants' claimed subject
matter under the 2019 Guidelines. Under Step 2A, prong one, of Guidelines,
we agree with the Examiner that claim 39 recites the judicial exception of a
natural phenomenon. (See 84 Fed. Reg. at 54.) The Specification
acknowledges that cf-DNA from two different individuals can naturally
occur in one individual, e.g., a pregnant woman or bone marrow transplant
recipient, is a known biological phenomenon. (See Spec. ,r 2.) The
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Specification also acknowledges that DNA methylation is a well-known
naturally occurring phenomenon. (See id. ,r 5.) Combining the two
biological processes, we find the claims recite the natural phenomenon that
methylated and unmethylated cf-DNA from two different individuals are
present in a sample from a single individual, e.g., a pregnant women or bone
marrow transplant recipient. Thus, like the determination in Ariosa that
claims to detecting paternally inherited nucleic acid of fetal origin from a
sample from a pregnant female are directed to a naturally occurring
phenomema, Appellants' currently pending claims also recite a naturally-
occurring phenomena. (See Ariosa, 788 F.3d 1376.)
We next evaluate whether the judicial exception is integrated into a
practical application in the second prong of Step 2A. (See 84 Fed. Reg. at
54.) For example, a claim element that applies the judicial exception to
effect a particular treatment or prophylaxis of disease or medical condition
may integrate a natural phenomenon into a practical application. (See id. at
55 (citing Vanda Pharm. Inc. v. West-Ward Pharm. Int'! Ltd., 887 F.3d
1117, 1135 (Fed. Cir. 2018)(holding that method of treatment by
administering drug at certain dosage ranges based on a patient's genotype
was not directed to a natural law)).) Likewise, a claimed advance that
harnesses a natural law to produce a technological improvement may be
patent eligible. See Athena Diagnostics, Inc. v. Mayo Collaborative
Services, LLC, 915 F.3d 743, 750 (Fed. Cir. 2019). However, steps that
merely apply conventional techniques to detect a natural law do not integrate
the judicial exception into a practical application. (Id. at 751 ("cfaims that
merely recite observing naturally occun-ing biological con-elations 'with no
meaningful non-routine steps in between' are directed to a natural law"
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(quoting Cleveland Clinic Found. v. True Health Diagnostics, LLC, 859
F.3d 1352, 1361 )).)
We agree with the Examiner that the claimed method does nothing
more than observe and identify the natural phenomenon. (See Examiner's
Answer issued December 19, 2017 ("Ans.") 16-17.) Claim 39 recites the
following steps to determine methylation status: 1) obtain a sample that
contains cf-DNA originated from two different individuals; 2) treat the cf-
DNA with a methylation specific reagent; 3) detect the presence of reacted
or unreacted cf-DNA. As in Athena, claim 39 then concludes in a "thereby
... " clause with a statement of the natural phenomenon, i.e., determining
methylation status of the DNA. See Athena, 915 F.3d at 751. The steps do
not include a practical application of the natural phenomenon. Because the
additional elements of the claim do not integrate the natural phenomenon
into a practical application, we find that the claim is directed to the judicial
exception.
As claim 39 is directed to a judicial exception under the first step of
the Alice/ Mayo test, we must evaluate whether the claim provides an
inventive concept, i.e., whether the additional elements amount to
significantly more than the exception itself. (See 2019 Guidelines, 84 Fed.
Reg. at 56.) As discussed above, the Examiner found the additional steps
describing the methylation analysis, e.g., treating and detecting, were well-
known, routine, and conventional. (See Final Act. 6-10.)
Appellants argue that the "established novelty of the claimed method
comprising these particular detection steps would support the notion that the
claim contains substantially more than merely a judicial exception." (Reply
Br. 4.) We are not persuaded. The Specification describes the steps of the
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claimed process to observe the natural law as standard techniques applied in
a standard way. For example, the treating step, e.g., bisulfite modification,
"was performed using a CpGenome DNA Modification Kit (Intergen) as
instructed by the manufacturer." (Spec. ,r 44.) Likewise, the detecting step,
e.g., Methylation-specific PCR, was "modified from the protocol as
described (Herman et al. 1996)." (Id. ,r 45.) The only remaining step of the
claim is identifying a sample of cf-DNA that contains methylated and
unmethylated DNA. However, "[t]he inventive concept necessary at step
two cannot be furnished by the unpatentable law of nature itself." Athena,
915 F.3d at 754. We agree with the Examiner that the method at issue in
Appellants' claims amounts to general instructions to practitioners to apply
routine, conventional techniques when seeking to detect methylated and
unmethylated cfIDNA and determine its methylation status. (See Ans. 10.)
Therefore, we find the claim does not provide additional elements that
amount to significantly more than the exception itself.
Because we conclude that the natural phenomenon recited in claim 39
is not integrated into a practical application and does not provide an
inventive concept, we conclude that the claimed method is not eligible.
Thus, we sustain the Examiner's§ 101 rejection of claims 39-56 as being
drawn to patent-ineligible subject matter.
35 U.S. C. § 102(b), Anticipation
The Examiner rejects claims 39--41, 48, 49, 54, 55 under 35 U.S.C
§ 102(b) as anticipated by Lo Coco. (Final Act. 12-13.) The Examiner
rejects claims 39--44, 49, 50, 52, 53 under 35 U.S.C. § 102(b) as anticipated
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by Turhan. 5 (Final Act. 13-14.) Because the same issue applies to both
rejections, we discuss the rejections together.
The Examiner finds Lo Coco discloses detecting methylated and
unmethylated DNA in bone marrow transplant recipients. (Final Act. 12-
13.) Although Lo Coco discloses obtaining DNA species originating from
cells of different individuals, the Examiner argues "[ o ]nee the DNA is
extracted it is a cell-free sample." (Id.)
The Examiner finds Turhan discloses DNA methylation analysis of a
pregnant woman. (Final Act. 14.) Although Turhan discloses analysis of
bone marrow and peripheral blood samples, the Examiner argues "Turhan
teaches obtaining DNA by extraction, thus, the sample is cell free." (Id.)
Appellants argue that "[n]either "Lo Coco nor Turhan teaches the
analysis of cell-free human DNA species." (Reply Br. 5, emphasis in
original.) Appellants argue "[t]o construe the term to also mean a human
DNA species that is located within cells as it is originally present in a
biological sample, i.e., a cellular human DNA species, would equate 'a cell-
free human DNA species in a biological sample'" with 'a human DNA
species in a biological sample,' thus effectively rendering the claim
limitation 'cell-free' completely meaningless. (Reply Br. 6., emphasis in
original.)
We are persuaded by Appellants' argument. The broadest reasonable
interpretation of a claim must be consistent with the interpretation of one of
5 Claims 52 and 53 depend from claim 51, which depends from claim 39.
The Examiner does not list claim 51 in the anticipation rejection over
Turhan. Because both the rejection of claims 52 and 53 and the prior art
were presented to Appellants, we find the error to be harmless.
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ordinary skill in the art. See In re Sneed, 710 F.2d 1544, 1548 (Fed. Cir.
1983). As argued by Appellants, the term "cell-free human DNA" would be
interpreted by one of ordinary skill in the art to be distinct from DNA
extracted from cells. Applying this interpretation, we find that neither Lo
Coco nor Turhan teach obtaining a biological sample containing cell-free
human DNA. Therefore, we find the Examiner erred in rejecting the claims
as anticipated and we reverse the rejection.
Obviousness-Type Double Patenting
The Examiner rejects claims 39-56 under the doctrine of obviousness-
type double patenting. (Final Act. 15-16.) In particular, the Examiner
rejects claims 39-56 as being unpatentable over claims 1-14 of U.S. Patent
No. 8,962,280; claims 1, 3, 5-7, 24--26 of U.S. Patent No. 6,927,028; claims
1-9 of U.S. Patent No. 8,431,343; claims 1-5 of U.S. Patent No. 7,709,197;
claims 1-27 of U.S. Patent No. 7,901,884; and claims 1-22 of U.S. Patent
No. 8,026,067. (See Final Act. 15-24.)
Appellants do not appeal the double patenting rejection. (See App.
Br. 5.) We consequently summarily affirm the Examiner's rejections on this
ground. (See 37 C.F.R. § 4I.37(c)(l)(iv) ("[A]ny arguments or authorities
not included in the appeal brief will be refused consideration by the Board
for purposes of the present appeal")).
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Conclusion
Upon consideration of the record and the reasons given, the
Examiner's rejection of claims 39-56 under 35 U.S.C. § 101 is sustained;
the Examiner's rejection of claims 39--41, 48, 49, 54, and 55 under 35
U.S.C. § 102(b) over Lo Coco is not sustained;
the Examiner's rejection of claims 39--44, 49, 50, 52, and 53 under 35
U.S.C. § 102(b) over Turhan is not sustained; and
the Examiner's rejections of claims 39-56 under obviousness-type
double patenting are sustained.
Therefore, we affirm the decision of the Examiner.
No time period for taking any subsequent action in connection with
this appeal may be extended under 3 7 C.F .R. § 1.13 6.
AFFIRMED
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